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https://www.readbyqxmd.com/read/28445990/prognostic-value-of-tumor-mutations-in-radically-treated-locally-advanced-non-small-cell-lung-cancer-patients
#1
Angela Boros, Ludovic Lacroix, Benjamin Lacas, Julien Adam, Jean-Pierre Pignon, Caroline Caramella, David Planchard, Vincent de Montpreville, Eric Deutsch, Antonin Levy, Benjamin Besse, Cécile Le Pechoux
INTRODUCTION: Chemo-radiation is standard treatment in locally advanced non-small cell lung cancers (NSCLC). The prognostic value of mutations has been poorly explored in this population. RESULTS: Clinical data were collected from 190 patients and mutational profiles were obtained in 78 of them; 58 (74%) were males, 31 (40%) current smokers, 47/31 stage IIIA/IIIB and 40 (51%) adenocarcinoma. The following mutations were identified: EGFR 12% (9/78), KRAS 15% (12/78), BRAF 5% (3/65), PI3KCA 2% (1/57), NRAS 3% (1/32), and ALK+ (FISH) 4% (2/51)...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445943/a-molecular-inversion-probe-based-next-generation-sequencing-panel-to-detect-germline-mutations-in-chinese-early-onset-colorectal-cancer-patients
#2
Junxiao Zhang, Xiaoyan Wang, Richarda M de Voer, Jayne Y Hehir-Kwa, Eveline J Kamping, Robbert D A Weren, Marcel Nelen, Alexander Hoischen, Marjolijn J L Ligtenberg, Nicoline Hoogerbrugge, Xiangling Yang, Zihuan Yang, Xinjuan Fan, Lei Wang, Huanliang Liu, Jianping Wang, Roland P Kuiper, Ad Geurts van Kessel
The currently known Mendelian colorectal cancer (CRC) predisposition syndromes account for ~5-10% of all CRC cases, and are caused by inherited germline mutations in single CRC predisposing genes. Using molecular inversion probes (MIPs), we designed a targeted next-generation sequencing panel to identify mutations in seven CRC predisposing genes: APC, MLH1, MSH2, MSH6, PMS2, MUTYH and NTHL1. From a consecutive series of 2,371 Chinese CRC patients, 140 familial and non-familial cases were selected that were diagnosed with CRC at or below the age of 35 years...
April 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28445521/next-generation-sequencing-to-dissect-the-genetic-architecture-of-kng1-and-f11-loci-using-factor-xi-levels-as-an-intermediate-phenotype-of-thrombosis
#3
Laura Martin-Fernandez, Giovana Gavidia-Bovadilla, Irene Corrales, Helena Brunel, Lorena Ramírez, Sonia López, Juan Carlos Souto, Francisco Vidal, José Manuel Soria
Venous thromboembolism is a complex disease with a high heritability. There are significant associations among Factor XI (FXI) levels and SNPs in the KNG1 and F11 loci. Our aim was to identify the genetic variation of KNG1 and F11 that might account for the variability of FXI levels. The KNG1 and F11 loci were sequenced completely in 110 unrelated individuals from the GAIT-2 (Genetic Analysis of Idiopathic Thrombophilia 2) Project using Next Generation Sequencing on an Illumina MiSeq. The GAIT-2 Project is a study of 935 individuals in 35 extended Spanish families selected through a proband with idiopathic thrombophilia...
2017: PloS One
https://www.readbyqxmd.com/read/28445096/protection-from-oxidative-stress-in-immunocytes-of-the-colonial-ascidian-botryllus-schlosseri-transcript-characterization-and-expression-studies
#4
Nicola Franchi, Francesca Ballin, Loriano Ballarin
Botryllus schlosseri is a cosmopolitan colonial ascidian that undergoes cyclical generation changes, or take-overs, during which adult zooids are resorbed and replaced by their buds. At take-over, adult tissues undergo diffuse apoptosis and effete cells are massively ingested by circulating phagocytes, with a consequent increase in oxygen consumption and in production of reactive oxygen species (ROS). The latter are responsible for the death of phagocytes involved in the clearance of apoptotic cells and corpses by phagocytosis-induced apoptosis...
February 2017: Biological Bulletin
https://www.readbyqxmd.com/read/28445014/detection-of-immunoglobulin-heavy-chain-gene-clonality-by-next-generation-sequencing-for-minimal-residual-disease-monitoring-in-b-lymphoblastic-leukemia
#5
Saeam Shin, In Sik Hwang, Jieun Kim, Kyung A Lee, Seung Tae Lee, Jong Rak Choi
Minimal residual disease (MRD) following B-lymphoblastic leukemia (B-ALL) treatment has gained prognostic importance. Clonal immunoglobulin heavy chain (IGH) gene rearrangement is a useful follow-up marker in B-ALL owing to its high positivity rate. We evaluated the performance and clinical applicability of a next-generation sequencing (NGS) assay for IGH rearrangement in B-ALL MRD monitoring. IGH rearrangement was tested by using fluorescence PCR-fragment analysis and the NGS assay in eight B-ALL patients...
July 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/28444508/study-protocol-on-the-role-of-intestinal-microbiota-in-colorectal-cancer-treatment-a-pathway-to-personalized-medicine-2-0
#6
R Aarnoutse, J M P G M de Vos-Geelen, J Penders, E G Boerma, F A R M Warmerdam, B Goorts, S W M Olde Damink, Z Soons, S S M Rensen, M L Smidt
PURPOSE: Investigate in patients with metastatic and/or irresectable colorectal cancer treated with systemic treatment with capecitabine or TAS-102 whether: 1. Intestinal microbiota composition can act as a predictor for response. 2. Intestinal microbiota composition changes during systemic treatment and its relation to chemotoxicity. BACKGROUND: Gut microbiota and host determinants evolve in symbiotic and dependent relationships resulting in a personal ecosystem...
April 25, 2017: International Journal of Colorectal Disease
https://www.readbyqxmd.com/read/28444304/a-frequent-oligogenic-involvement-in-congenital-hypothyroidism
#7
Tiziana de Filippis, Giulia Gelmini, Elvezia Paraboschi, Maria Cristina Vigone, Marianna Di Frenna, Federica Marelli, Marco Bonomi, Alessandra Cassio, Daniela Larizza, Mirella Moro, Giorgio Radetti, Mariacarolina Salerno, Diego Ardissino, Giovanna Weber, Davide Gentilini, Fabiana Guizzardi, Stefano Duga, Luca Persani
Congenital Hypothyroidism (CH), the most frequent form of preventable mental retardation, is predicted to have a relevant genetic origin. However, CH is frequently reported to be sporadic and candidate gene variations were found in < 10% of the investigated patients. Here, we characterize the involvement of 11 candidate genes through a systematic Next Generation Sequencing (NGS) analysis. The NGS was performed in 177 unrelated CH patients (94 gland-in-situ; 83 dysgenesis) and in 3,538 control subjects...
April 21, 2017: Human Molecular Genetics
https://www.readbyqxmd.com/read/28444293/regulation-of-hematopoiesis-and-immune-responses-by-long-noncoding-rnas
#8
Wooseok Seo, Ichiro Taniuchi
Since the first draft of the human genome sequence was released in 2001, unprecedentedly rapid progress has been made in whole genome-wide approaches by utilizing next-generation-sequencing technologies. The last decade alone has generated enormous data in the forms of exome sequencing, transcriptomes, transcription factor occupancy, genomic variation profiling and epigenetic modifications. One of the most striking realizations from sequencing studies has been the discovery and characterization of noncoding RNAs...
April 22, 2017: International Immunology
https://www.readbyqxmd.com/read/28443097/large-diversity-of-functional-nanobodies-from-a-camelid-immune-library-revealed-by-an-alternative-analysis-of-next-generation-sequencing-data
#9
Pieter Deschaght, Ana Paula Vintém, Marc Logghe, Miguel Conde, David Felix, Rob Mensink, Juliana Gonçalves, Jorn Audiens, Yanik Bruynooghe, Rita Figueiredo, Diana Ramos, Robbe Tanghe, Daniela Teixeira, Liesbeth Van de Ven, Catelijne Stortelers, Bruno Dombrecht
Next-generation sequencing (NGS) has been applied successfully to the field of therapeutic antibody discovery, often outperforming conventional screening campaigns which tend to identify only the more abundant selective antibody sequences. We used NGS to mine the functional nanobody repertoire from a phage-displayed camelid immune library directed to the recepteur d'origine nantais (RON) receptor kinase. Challenges to this application of NGS include accurate removal of read errors, correct identification of related sequences, and establishing meaningful inclusion criteria for sequences-of-interest...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28442638/deep-sequencing-of-the-transcriptome-in-the-anterior-pituitary-of-heifers-before-and-after-ovulation
#10
Kiran Pandey, Yoichi Mizukami, Kenji Watanabe, Syuiti Sakaguti, Hiroya Kadokawa
We aimed to determine gene expression patterns in the anterior pituitary (AP) of heifers before and after ovulation via deep sequencing of the transcriptome (RNA-seq) to identify new genes and clarify important pathways. Heifers were slaughtered on the estrus day (pre-ovulation; n=5) or 3 days after ovulation (post-ovulation; n=5) for AP collection. We randomly selected 4 pre-ovulation and 4 post-ovulation APs, and the ribosomal RNA-depleted poly (A)+RNA were prepared to assemble next-generation sequencing libraries...
April 23, 2017: Journal of Veterinary Medical Science
https://www.readbyqxmd.com/read/28442608/unexpected-relations-of-historical-anthrax-strain
#11
M H Antwerpen, J W Sahl, D Birdsell, T Pearson, M J Pearce, C Redmond, H Meyer, P S Keim
In 1998, it was claimed that an 80-year-old glass tube intentionally filled with Bacillus anthracis and embedded in a sugar lump as a WWI biological weapon still contained viable spores. Today, genome sequencing of three colonies isolated in 1998 and subjected to phylogenetic analysis surprisingly identified a well-known B. anthracis reference strain isolated in the United States in 1981, pointing to accidental laboratory contamination.IMPORTANCE Next-generation sequencing and subsequent phylogenetic analyses are useful and reliable tools for the classification of recent and historical samples...
April 25, 2017: MBio
https://www.readbyqxmd.com/read/28442586/therapeutic-targeting-of-ptk7-is-cytotoxic-in-atypical-teratoid-rhabdoid-tumors
#12
Shanta M Messerli, Mariah M Hoffman, Etienne Z Gnimpieba, Ratan D Bhardwaj
Novel discoveries involving the evaluation of potential therapeutics are based on newly identified molecular targets for atypical teratoid rhabdoid tumors (ATRT), which are the most common form of infantile brain tumors. Central nervous system ATRTs are rare, aggressive, and fast growing tumors of the brain and spinal cord and carry a very poor prognosis. Currently, the standard of care for ATRT patients is based on surgical resection followed by systemic chemotherapy and radiation therapy, which result in severe side effects...
April 25, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28442585/next-gen-sequencing-analysis-and-algorithms-for-pdx-and-cdx-models
#13
Garima Khandelwal, Maria Romina Girotti, Christopher Smowton, Sam Taylor, Chris Wirth, Marek Dynowski, Kristopher K Frese, Ged Brady, Caroline Dive, Richard Marais, Crispin Miller
Patient-derived xenograft (PDX) and CTC-derived explant (CDX) models are powerful methods for the study of human disease. In cancer research, these methods have been applied to multiple questions including the study of metastatic progression, genetic evolution and therapeutic drug responses. Since PDX and CDX models can recapitulate the highly heterogeneous characteristics of a patient tumor, as well as their response to chemotherapy, there is considerable interest in combining them with next-generation sequencing (NGS) in order to monitor the genomic, transcriptional, and epigenetic changes that accompany oncogenesis...
April 25, 2017: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/28442298/how-to-study-and-overcome-tumor-heterogeneity-with-circulating-biomarkers-the-breast-cancer-case
#14
REVIEW
Valentina Appierto, Serena Di Cosimo, Carolina Reduzzi, Valentina Pala, Vera Cappelletti, Maria Grazia Daidone
Breast cancer ranks first among female cancer-related deaths in Western countries. As the primary tumor can often be controlled by surgical resection, the survival of women with breast cancer is closely linked to the incidence of distant metastases. Molecular screening by next generation sequencing highlighted the spatial and temporal heterogeneity of solid tumors as well as the clonal evolution of cancer cells during progression and under treatment pressure. Such findings question whether an optimal assessment of disease progression and a screening for druggable mutations should be based on molecular features of primary or recurrent/metastatic lesions and therefore represent a crucial element for failure or success of personalized medicine...
April 22, 2017: Seminars in Cancer Biology
https://www.readbyqxmd.com/read/28442289/hla-a-b-and-c-allele-and-haplotype-frequencies-defined-by-next-generation-sequencing-in-a-population-of-519-english-blood-donors
#15
Sue Davey, John Ord, Cristina Navarrete, Colin Brown
Whole gene next generation sequencing was used to determine the HLA class I haplotype and allele frequencies in a cohort of 519 English blood donors. This is the first report of HLA frequencies at third field resolution in a UK population with a total of 33, 52 and 30 alleles identified for HLA-A, -B and -C, respectively. Of the 1411 haplotypes determined, 281 had a frequency of greater than 0.05%. Data are available from the Allele Frequencies Net Database under the population name 'England Blood Donors of Mixed Ethnicity', identifier 3392...
April 22, 2017: Human Immunology
https://www.readbyqxmd.com/read/28442211/leigh-like-neuroimaging-features-associated-with-new-biallelic-mutations-in-opa1
#16
Anna Rubegni, Tiziana Pisano, Giacomo Bacci, Alessandra Tessa, Roberta Battini, Elena Procopio, Sabrina Giglio, Rosa Pasquariello, Filippo Maria Santorelli, Renzo Guerrini, Claudia Nesti
Behr syndrome is characterized by the association of early onset optic atrophy, cerebellar ataxia, pyramidal signs, peripheral neuropathy and mental retardation. Recently, some cases were reported to be caused by biallelic mutations in OPA1. We describe an 11-year-old girl (Pt1) and a 7-year-old boy (Pt2) with cognitive delay, ataxic gait and clinical signs suggestive of a peripheral neuropathy, with onset in early infancy. In Pt1 ocular fundus examination revealed optic disk pallor whereas Pt2 exhibited severe optic atrophy...
April 15, 2017: European Journal of Paediatric Neurology: EJPN
https://www.readbyqxmd.com/read/28442200/next-generation-sequencing-and-culture-based-techniques-offer-complementary-insights-into-fungi-and-prokaryotes-in-beach-sands
#17
Daniela Romão, Christopher Staley, Filipa Ferreira, Raquel Rodrigues, Raquel Sabino, Cristina Veríssimo, Ping Wang, Michael Sadowsky, João Brandão
A next-generation sequencing (NGS) approach, in conjunction with culture-based methods, was used to examine fungal and prokaryotic communities for the presence of potential pathogens in beach sands throughout Portugal. Culture-based fungal enumeration revealed low and variable concentrations of the species targeted (yeasts and dermatophytes), which were underrepresented in the community characterized by NGS targeting the ITS1 region. Conversely, NGS indicated that the potentially pathogenic species Purpureocillium liliacinum comprised nearly the entire fungal community...
April 23, 2017: Marine Pollution Bulletin
https://www.readbyqxmd.com/read/28442163/the-search-for-the-missing-heritability-of-prostate-cancer
#18
EDITORIAL
Patrick C Walsh
Scientists and clinicians at Johns Hopkins have been working since 1987 to uncover the genetic pathogenesis of prostate cancer. A patient query about the hereditary nature of the disease led to data collection on family history, followed by segregation and linkage analyses. Collaborative investigations using next-generation sequencing to identify genetic variants associated with prostate cancer risk have revealed the significance of HOXB13, BRCA 1/2, and DNA repair mutations.
April 22, 2017: European Urology
https://www.readbyqxmd.com/read/28441826/-a-childhood-onset-rapid-onset-dystonia-parkinsonism-family-with-atp1a3-gene-mutation-and-literatures-review
#19
C L Zhang, F Yin, F He, N Gai, Z Q Shi, J Peng
Objective: To explore clinical characteristics, treatment, and prognosis of a family with childhood-onset rapid-onset dystonia parkinsonism (RDP) caused by ATP1A3 gene mutation and review literatures. Method: The clinical data of a RDP child, his brother and mother had been analyzed retrospectively. This family was admitted to Xiangya Hospital in January 2016. DNA samples were analyzed by the next-generation sequencing and confirmed by Sanger sequencing. Related literature from PubMed, Online Mendelian Inheritance in Man (OMIM), CNKI and Wanfang databases to date (up to October 2016) with"Rapid-onset dystonia-parkinsonism"RDP"DYT12" as key words was reviewed...
April 2, 2017: Zhonghua Er Ke za Zhi. Chinese Journal of Pediatrics
https://www.readbyqxmd.com/read/28441149/epigenetic-regulatory-mutations-and-epigenetic-therapy-for-multiple-myeloma
#20
Daphné Dupéré-Richer, Jonathan D Licht
PURPOSE OF REVIEW: Next generation sequencing and large-scale analysis of patient specimens has created a more complete picture of multiple myeloma (MM) revealing that epigenetic deregulation is a prominent factor in MM pathogenesis. RECENT FINDINGS: Over half of MM patients have mutations in genes encoding epigenetic modifier enzymes. The DNA methylation profile of MM is related to the stage of the disease and certain classes of mutations in epigenetic modifiers are more prevalent upon disease relapse, suggesting a role in disease progression...
April 22, 2017: Current Opinion in Hematology
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